search

t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
37 stars 22 forks source link

ReadCount to get number of reads mapped? #113

Closed my-linh-luu closed 5 months ago

my-linh-luu commented 2 years ago

Hello,

I have a question about the ReadCount column obtained in the TCcount CSV file. I thought I would get the number of reads that were mapped by summing all the read counts obtained. However, with this method, I get a higher number of reads than what was given initially with no multimap. Do you have any idea about this?

Thank you

t-neumann commented 2 years ago

I don't know what exactly you mean by "given intially with no multimap"?

One thing I can think of is that you have overlapping intervals in the bed file so reads are counted multiple times.

my-linh-luu commented 2 years ago

Hi, It was indeed an issue with our data.

Thank you.